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The museum was formally founded on 10 June 1793, during the French Revolution. Its origins lie, however, in the Jardin royal des plantes médicinales (Royal Medicinal Plant Garden) created by King Louis XIII in 1635, which was directed and run by the royal physician.

The royal institution remarkably survived the French Revolution by being reorganized in 1793 as a republican Muséum national d'Histoire naturelle with twelve professorships of equal rank. Some of its early professors included eminent comparative anatomist Georges Cuvier and evolutionary pioneers Jean-Baptiste de Lamarck and Étienne Geoffroy Saint-Hilaire. The museum's aims were to instruct the public, put together collections and conduct scientific research. It continued to flourish during the 19th century.

The galleries open to the public are the Cabinet d’Histoire du Jardin des Plantes in the Hôtel de Magny, the Gallery of Mineralogy and Geology, the Gallery of Palaeontology and Comparative Anatomy, and the famous Grand Gallery of Evolution (Grande Galerie de l'évolution). The museum's Menagerie is also located here. The collections are vast and cover several field of Natural History, from mummies to fossils, insects to mollusk, vegetals, artworks...

In recent decades, it has directed its research and education efforts at the effects of human exploitation on the environment.